For some intelligence officials, proof that the CIA's influence on the U.S. war effort in Afghanistan is waning, and the power of the Pentagon is growing, came last summer when the CIA named its new station chief in Kabul.

As a rule, the CIA always gets to pick its chief of station in foreign countries, but in Afghanistan it lost a political battle to the military and the State Department. According to several former and current intelligence officials, that loss is symbolic of the declining influence of the CIA, which once shaped the strategy for the U.S. war effort.

Last summer, when the CIA tapped a veteran office to become the new chief of station in Kabul, the State Department's special envoy to Afghanistan, Richard Holbrooke, objected. According to current and former officials, Holbrooke had served with the officer in Croatia during the Balkan conflict in the 1990s, when the officer was station chief there and Holbrooke was the Clinton administration's special envoy to the region.

By the time Holbrooke weighed in privately to agency officials, the officer had already been told that he would be assigned to Afghanistan.

"Holbrooke had a problem with [the agency's choice]," said a current senior intelligence official. "And he told the Agency he wasn't going to work with [the CIA officer]."

A spokesperson for Ambassador Holbrooke denied Holbrooke's involvement in the CIA's decision.

In the past, say officials, the CIA wouldn't have backed down. Less than 10 years ago, the U.S. ambassador in France objected to the agency's choice of station chief. He said he didn't want to work with the agency's choice, and asked that he not be sent. The agency made its preferred candidate station chief anyway.

This time, though Kabul is one of the CIA's most important bases of operations, the agency acceded to State Department wishes and withdrew its candidate. Then Gen. Stanley McChrystal intervened.

According to the current and former intelligence officials, McChrystal, commander of U.S. and international forces in Afghanistan, had his own preferred candidate for the job, a good friend and decorated CIA paramilitary officer. McChrystal started lobbying for his friend.

'McChrystal Can Have Anyone He Wants'

The officer McChrystal preferred has extensive experience in war zones, including two previous tours in Afghanistan, as well as time in the Balkans, Baghdad and Yemen. The officer also served as the CIA's liaison to the Pentagon's Joint Special Operations Command (JSOC), then led by McChrystal. JSOC is the Pentagon's command structure for special forces from all military branches, including the Navy SEALs and the Army's Delta Force.

The officer had already served as Kabul's chief four years ago, and it is unusual, though not unprecedented, these intelligence officials say, for CIA officers to serve as chief of station twice in the same country. In interviews with a dozen current and former officials, the current chief of station was uniformly well-liked and admired. A career paramilitary officer, the station chief came to the CIA after several years in an elite Marine unit.

During the U.S. invasion of Afghanistan more than eight years ago, the CIA officer worked closely with McChrystal, who was then a commander of elite military commandos. The CIA official is well known in CIA lore as the man who saved Hamid Karzai's life when the CIA led the effort to oust the Taliban from power in October 2001. Karzai is said to be greatly indebted to the CIA officer, and was pleased when the officer was named chief of station three years later.

In the end, however, the officials say, it was the CIA officer's long relationship with General McChrystal that was the deciding factor. Rather than find another candidate, the agency gave McChrystal's friend the job.

That McChrystal, an Army general, was able to install a friend as station chief, said a former official, was indicative of both McChrystal's pull and the reality of the Afghan war zone, where the military now has a greater presence than it did just a year ago. "McChrystal can have anyone he wants running the CIA station," said a former senior intelligence official who now consults for the Pentagon on Afghan issues.

Geoff Morrell, a Pentagon spokesman said, "As far as I know, just as the Defense Secretary picks his top commanders, the CIA Director picks his station chiefs."

According to two current and former intelligence officials, the official who was the agency's first choice told colleagues he was frustrated by the decision. Instead of going to Kabul, he kept his job as the chief official in the CIA's European operations division.

At the request of the CIA, ABC News is withholding the names of both the CIA's original choice for the job and the official who got the job because both are still undercover.

CIA spokesman George Little denied that Holbrooke or McChrystal had any involvement in the agency's decision.

"The CIA makes its own personnel decisions. Period. That's all there is to it." The intelligence officials, who requested anonymity when discussing sensitive personnel matters, have no problem with the officer who was eventually chosen by the agency. But they said the agency clearly preferred someone else, and they fear the CIA has become subordinate to the military, after many years dominating U.S .efforts in Afghanistan after the September 11th attacks.

'This Is a Sign of Things to Come'

"We were in the lead after the invasion, but clearly the CIA has taken more of a support role," said a former senior official who served in Afghanistan.

The current and former intelligence officials say that putting a paramilitary officer in charge on the Afghan base highlights the CIA's evolving role. The CIA's historic wartime role was collecting information in order to shape overall strategy. Now the agency has been relegated to a supporting role, supplying tactical intelligence to help the military. The military determines the strategy.

"The CIA is supposed to be a check on the military and their intelligence, not their hand maiden," said Robert Baer, a former CIA case officer. "This is a sign of things to come, where the military dominates intelligence."

The problem with this shift, the officials say, is that both the military and the CIA are focusing on short-term, tactical intelligence, and ignoring the long view. The shortfall in intelligence collection was highlighted last month in a public report by the military's top intelligence officer that was prepared for a thinktank. In the report, Major General Michael T. Flynn concluded that intelligence collection in Afghanistan was "only marginally relevant to the overall strategy."

Flynn's report was as critical of the CIA as of military intelligence. But it is the military that is now shaping intelligence collection in Afghanistan, in part through sheer numeric dominance. Military forces far outnumber the CIA, and the disproportion is growing. According to a current intelligence official, the CIA has roughly 800 personnel in Afghanistan scattered among 14 bases. By next summer, the military expects that it will have nearly 100,000 troops, roughly double its strength in early 2009.

Flynn concluded that the "vast intelligence apparatus is unable to answer fundamental questions about the environment in which the US and allied forces operate and the people they seek to persuade."